Boolean modifier not making new faces in mesh
The problems I have with booleans usually relate to two meshes having one or more vertices in the same place. You might be able to fix this by scaling one of the objects slightly, but this obviously will change its size. You might be able to manually move the offending vertices out of each others' way.
Another possibility is you created an object in an older version of Blender, and have now opened it in a newer version of Blender. The data structures are not the same, and booleans will give unexpected results.
Another thing you can try is to run the 3d printing checks, and fix any problems that crop up before applying your booleans.